Young but not relatively old retrotransposons are preferentially located in gene-rich euchromatic regions in tomato (Solanum lycopersicum) plants
文献类型： 外文期刊
作者： Xu, Yingxiu 1 ; Du, Jianchang 1 ;
作者机构： 1.Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;Key laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing 210014, China,
2.State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agriculture Sciences, Anyang 455000, China
关键词： targeting specificity;purifying selection;recombination;retrotransposon;tomato
期刊名称：PLANT JOURNAL （ 影响因子：6.417； 五年影响因子：7.627 ）
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收录情况： SCI
摘要： Long terminal repeat (LTR) retrotransposons are the major DNA components of flowering plants. They are generally enriched in pericentromeric heterochromatin regions of their host genomes, which could result from the preferential insertion of LTR retrotransposons and the low effectiveness of purifying selection in these regions. To estimate the relative importance of the actions of these two factors on their distribution pattern, the LTR retrotransposons in Solanum lycopersicum (tomato) plants were characterized at the genome level, and then the distribution of young elements was compared with that of relatively old elements. The current data show that old elements are mainly located in recombination-suppressed heterochromatin regions, and that young elements are preferentially located in the gene-rich euchromatic regions. Further analysis showed a negative correlation between the insertion time of LTR retrotransposons and the recombination rate. The data also showed there to be more solo LTRs in genic regions than in intergenic regions or in regions close to genes. These observations indicate that, unlike in many other plant genomes, the current LTR retrotransposons in tomatoes have a tendency to be preferentially located into euchromatic regions, probably caused by their severe suppression of activities in heterochromatic regions. These elements are apt to be maintained in heterochromatin regions, probably as a consequence of the pericentromeric effect in tomatoes. These results also indicate that local recombination rates and intensities of purifying selection in different genomic regions are largely responsible for structural variation and non-random distribution of LTR retrotransposons in tomato plants.
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